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<div class="title">moltk/PDBStructure.hpp</div>  </div>
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<a href="PDBStructure_8hpp.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/*</span>
<a name="l00002"></a>00002 <span class="comment">    MolTK is a Python and C++ toolkit for protein sequence/structure alignment and visualization</span>
<a name="l00003"></a>00003 <span class="comment">    Copyright (C) 2011  Christopher M. Bruns</span>
<a name="l00004"></a>00004 <span class="comment"></span>
<a name="l00005"></a>00005 <span class="comment">    This program is free software; you can redistribute it and/or modify</span>
<a name="l00006"></a>00006 <span class="comment">    it under the terms of the GNU General Public License as published by</span>
<a name="l00007"></a>00007 <span class="comment">    the Free Software Foundation; either version 2 of the License, or</span>
<a name="l00008"></a>00008 <span class="comment">    (at your option) any later version.</span>
<a name="l00009"></a>00009 <span class="comment"></span>
<a name="l00010"></a>00010 <span class="comment">    This program is distributed in the hope that it will be useful,</span>
<a name="l00011"></a>00011 <span class="comment">    but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00012"></a>00012 <span class="comment">    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
<a name="l00013"></a>00013 <span class="comment">    GNU General Public License for more details.</span>
<a name="l00014"></a>00014 <span class="comment"></span>
<a name="l00015"></a>00015 <span class="comment">    You should have received a copy of the GNU General Public License along</span>
<a name="l00016"></a>00016 <span class="comment">    with this program; if not, write to the Free Software Foundation, Inc.,</span>
<a name="l00017"></a>00017 <span class="comment">    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.</span>
<a name="l00018"></a>00018 <span class="comment">    </span>
<a name="l00019"></a>00019 <span class="comment">    Commercial users should ask about our dual licensing model.</span>
<a name="l00020"></a>00020 <span class="comment">    For questions contact: cmbruns@rotatingpenguin.com</span>
<a name="l00021"></a>00021 <span class="comment">*/</span>
<a name="l00022"></a>00022 
<a name="l00023"></a>00023 <span class="preprocessor">#ifndef MOLTK_CHEM_PDB_STRUCTURE_H</span>
<a name="l00024"></a>00024 <span class="preprocessor"></span><span class="preprocessor">#define MOLTK_CHEM_PDB_STRUCTURE_H</span>
<a name="l00025"></a>00025 <span class="preprocessor"></span>
<a name="l00026"></a>00026 <span class="preprocessor">#include &quot;<a class="code" href="Biosequence_8hpp.html">moltk/Biosequence.hpp</a>&quot;</span>
<a name="l00027"></a>00027 <span class="preprocessor">#include &quot;<a class="code" href="Printable_8hpp.html">moltk/Printable.hpp</a>&quot;</span>
<a name="l00028"></a>00028 <span class="preprocessor">#include &lt;iostream&gt;</span>
<a name="l00029"></a>00029 <span class="preprocessor">#include &lt;vector&gt;</span>
<a name="l00030"></a>00030 <span class="preprocessor">#include &lt;string&gt;</span>
<a name="l00031"></a>00031 
<a name="l00032"></a>00032 <span class="keyword">namespace </span>moltk {
<a name="l00033"></a>00033 
<a name="l00038"></a><a class="code" href="classmoltk_1_1PDBStructure.html">00038</a> <span class="keyword">class </span><a class="code" href="classmoltk_1_1PDBStructure.html" title="PDBStructure represents a macromolecule structure as found in a Protein Data Bank file...">PDBStructure</a>
<a name="l00039"></a>00039 {
<a name="l00040"></a>00040 <span class="keyword">public</span>:
<a name="l00044"></a><a class="code" href="classmoltk_1_1PDBStructure_1_1Atom.html">00044</a>     <span class="keyword">class </span><a class="code" href="classmoltk_1_1PDBStructure_1_1Atom.html" title="Structure::Atom represents a chemical atom in a molecular structure.">Atom</a>
<a name="l00045"></a>00045     {
<a name="l00046"></a>00046     <span class="keyword">public</span>:
<a name="l00047"></a><a class="code" href="classmoltk_1_1PDBStructure_1_1Atom.html#a70a2690f27ceeab8f42793db845fcc6f">00047</a>         <span class="keyword">enum</span> <a class="code" href="classmoltk_1_1PDBStructure_1_1Atom.html#a70a2690f27ceeab8f42793db845fcc6f">RecordType</a> {
<a name="l00048"></a><a class="code" href="classmoltk_1_1PDBStructure_1_1Atom.html#a70a2690f27ceeab8f42793db845fcc6fa24c6a40e9a6ed87f14acef0cffca1450">00048</a>             <a class="code" href="classmoltk_1_1PDBStructure_1_1Atom.html#a70a2690f27ceeab8f42793db845fcc6fa24c6a40e9a6ed87f14acef0cffca1450">RECORD_TYPE_ATOM</a>, <span class="comment">//&lt; Standard protein, DNA, or RNA atoms</span>
<a name="l00049"></a><a class="code" href="classmoltk_1_1PDBStructure_1_1Atom.html#a70a2690f27ceeab8f42793db845fcc6fa37d30cb507b3b11dbec9247306c9303f">00049</a>             <a class="code" href="classmoltk_1_1PDBStructure_1_1Atom.html#a70a2690f27ceeab8f42793db845fcc6fa37d30cb507b3b11dbec9247306c9303f">RECORD_TYPE_HETATM</a> <span class="comment">//&lt; Other atom types</span>
<a name="l00050"></a>00050         };
<a name="l00052"></a><a class="code" href="classmoltk_1_1PDBStructure_1_1Atom.html#a2284676e8460e244b9ac326a19b3e34f">00052</a>         <a class="code" href="classmoltk_1_1PDBStructure_1_1Atom.html#a70a2690f27ceeab8f42793db845fcc6f">RecordType</a> <a class="code" href="classmoltk_1_1PDBStructure_1_1Atom.html#a2284676e8460e244b9ac326a19b3e34f" title="Whether this is a standard macromolecule atom type (ATOM) or other (HETATM).">get_record_type</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1PDBStructure_1_1Atom.html#af755f6dac2b1915a257146662e3ae5e7">record_type</a>;}
<a name="l00053"></a>00053     
<a name="l00054"></a>00054     <span class="keyword">protected</span>:
<a name="l00055"></a><a class="code" href="classmoltk_1_1PDBStructure_1_1Atom.html#af755f6dac2b1915a257146662e3ae5e7">00055</a>         <a class="code" href="classmoltk_1_1PDBStructure_1_1Atom.html#a70a2690f27ceeab8f42793db845fcc6f">RecordType</a> <a class="code" href="classmoltk_1_1PDBStructure_1_1Atom.html#af755f6dac2b1915a257146662e3ae5e7">record_type</a>;
<a name="l00056"></a>00056     };
<a name="l00057"></a><a class="code" href="classmoltk_1_1PDBStructure.html#ad5de261e14b5095d93a495e27351777b">00057</a>     <span class="keyword">typedef</span> std::vector&lt;Atom&gt; <a class="code" href="classmoltk_1_1PDBStructure.html#ad5de261e14b5095d93a495e27351777b">AtomList</a>;
<a name="l00058"></a>00058 
<a name="l00059"></a>00059 
<a name="l00064"></a><a class="code" href="classmoltk_1_1PDBStructure_1_1Residue.html">00064</a>     <span class="keyword">class </span><a class="code" href="classmoltk_1_1PDBStructure_1_1Residue.html" title="Residue represents a single amino acid or nucleotide residue, or a small molecule, in a macromolecule structure.">Residue</a> : <span class="keyword">public</span> <a class="code" href="classmoltk_1_1BaseBiosequence.html" title="Parent class for macromolecule sequences and structures.">BaseBiosequence</a>::BaseResidue
<a name="l00065"></a>00065     {
<a name="l00066"></a>00066     <span class="keyword">public</span>:
<a name="l00067"></a><a class="code" href="classmoltk_1_1PDBStructure_1_1Residue.html#a8c4d00bb882865dd5f964c574e1190b8">00067</a>         <a class="code" href="classmoltk_1_1PDBStructure_1_1Residue.html#a8c4d00bb882865dd5f964c574e1190b8">Residue</a>() {}
<a name="l00068"></a><a class="code" href="classmoltk_1_1PDBStructure_1_1Residue.html#a9544c5eca44265e02aca051f75788315">00068</a>         <a class="code" href="classmoltk_1_1PDBStructure_1_1Residue.html#a8c4d00bb882865dd5f964c574e1190b8">Residue</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1PDBStructure_1_1Residue.html" title="Residue represents a single amino acid or nucleotide residue, or a small molecule, in a macromolecule structure.">Residue</a>&amp; rhs)
<a name="l00069"></a>00069             : <a class="code" href="classmoltk_1_1PDBStructure_1_1Residue.html#a3c8100085d64fb0b54fc90358af3c327">one_letter_code</a>(rhs.<a class="code" href="classmoltk_1_1PDBStructure_1_1Residue.html#a3c8100085d64fb0b54fc90358af3c327">one_letter_code</a>)
<a name="l00070"></a>00070             , <a class="code" href="classmoltk_1_1PDBStructure_1_1Residue.html#af013d260c48c242417b7e4a16900be33">residue_number</a>(rhs.<a class="code" href="classmoltk_1_1PDBStructure_1_1Residue.html#af013d260c48c242417b7e4a16900be33">residue_number</a>)
<a name="l00071"></a>00071         {}
<a name="l00072"></a><a class="code" href="classmoltk_1_1PDBStructure_1_1Residue.html#aed00039c0a6da6e4e5a83d23ec898c98">00072</a>         <span class="keyword">virtual</span> <span class="keywordtype">char</span> <a class="code" href="classmoltk_1_1PDBStructure_1_1Residue.html#aed00039c0a6da6e4e5a83d23ec898c98">get_one_letter_code</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1PDBStructure_1_1Residue.html#a3c8100085d64fb0b54fc90358af3c327">one_letter_code</a>;}
<a name="l00073"></a><a class="code" href="classmoltk_1_1PDBStructure_1_1Residue.html#a95335a7d300e9821bdbffb7b3a35060e">00073</a>         <span class="keyword">virtual</span> <span class="keywordtype">int</span> <a class="code" href="classmoltk_1_1PDBStructure_1_1Residue.html#a95335a7d300e9821bdbffb7b3a35060e">get_residue_number</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1PDBStructure_1_1Residue.html#af013d260c48c242417b7e4a16900be33">residue_number</a>;}
<a name="l00074"></a>00074 
<a name="l00075"></a>00075     <span class="keyword">protected</span>:
<a name="l00076"></a><a class="code" href="classmoltk_1_1PDBStructure_1_1Residue.html#a3c8100085d64fb0b54fc90358af3c327">00076</a>         <span class="keywordtype">char</span> <a class="code" href="classmoltk_1_1PDBStructure_1_1Residue.html#a3c8100085d64fb0b54fc90358af3c327">one_letter_code</a>;
<a name="l00077"></a><a class="code" href="classmoltk_1_1PDBStructure_1_1Residue.html#af013d260c48c242417b7e4a16900be33">00077</a>         <span class="keywordtype">int</span> <a class="code" href="classmoltk_1_1PDBStructure_1_1Residue.html#af013d260c48c242417b7e4a16900be33">residue_number</a>;
<a name="l00078"></a>00078     };
<a name="l00079"></a>00079 
<a name="l00083"></a><a class="code" href="classmoltk_1_1PDBStructure_1_1Chain.html">00083</a>     <span class="keyword">class </span><a class="code" href="classmoltk_1_1PDBStructure_1_1Chain.html" title="Chain represents a single polymer or molecule in a PDBStructure.">Chain</a> : <span class="keyword">public</span> <a class="code" href="classmoltk_1_1BaseBiosequence.html" title="Parent class for macromolecule sequences and structures.">BaseBiosequence</a>
<a name="l00084"></a>00084     {
<a name="l00085"></a>00085     <span class="keyword">public</span>:
<a name="l00086"></a><a class="code" href="classmoltk_1_1PDBStructure_1_1Chain.html#acbbbb6eba40ef9cd1ac8123ca4bbd453">00086</a>         <a class="code" href="classmoltk_1_1PDBStructure_1_1Chain.html#acbbbb6eba40ef9cd1ac8123ca4bbd453">Chain</a>() {}
<a name="l00087"></a><a class="code" href="classmoltk_1_1PDBStructure_1_1Chain.html#a08a5fd5b7db7c07432c777b69a6467ce">00087</a>         <a class="code" href="classmoltk_1_1PDBStructure_1_1Chain.html#a08a5fd5b7db7c07432c777b69a6467ce">Chain</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1PDBStructure_1_1Chain.html" title="Chain represents a single polymer or molecule in a PDBStructure.">Chain</a>&amp; rhs) : <a class="code" href="classmoltk_1_1PDBStructure_1_1Chain.html#a759a8771e9442c21cf51fc1a140c3216">residues</a>(rhs.<a class="code" href="classmoltk_1_1PDBStructure_1_1Chain.html#a759a8771e9442c21cf51fc1a140c3216">residues</a>) {}
<a name="l00088"></a><a class="code" href="classmoltk_1_1PDBStructure_1_1Chain.html#acbde49bcc732f9830a3c1d60e37c0644">00088</a>         <span class="keyword">virtual</span> <span class="keywordtype">size_t</span> <a class="code" href="classmoltk_1_1PDBStructure_1_1Chain.html#acbde49bcc732f9830a3c1d60e37c0644">get_number_of_residues</a>()<span class="keyword"> const </span>{<span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1PDBStructure_1_1Chain.html#a759a8771e9442c21cf51fc1a140c3216">residues</a>.size();}
<a name="l00089"></a><a class="code" href="classmoltk_1_1PDBStructure_1_1Chain.html#a24980b95a88bb1476c283a6f91944a2c">00089</a>         <span class="keyword">virtual</span> <span class="keyword">const</span> <a class="code" href="classmoltk_1_1BaseBiosequence_1_1BaseResidue.html" title="Parent class for macromolecule sequence residues (nucleotides or amino acids)">BaseResidue</a>&amp; <a class="code" href="classmoltk_1_1PDBStructure_1_1Chain.html#a24980b95a88bb1476c283a6f91944a2c">get_residue</a>(<span class="keywordtype">size_t</span> index)<span class="keyword"> const </span>{
<a name="l00090"></a>00090             <span class="keywordflow">return</span> <a class="code" href="classmoltk_1_1PDBStructure_1_1Chain.html#a759a8771e9442c21cf51fc1a140c3216">residues</a>[index];
<a name="l00091"></a>00091         }
<a name="l00092"></a>00092     <span class="keyword">protected</span>:
<a name="l00093"></a><a class="code" href="classmoltk_1_1PDBStructure_1_1Chain.html#a759a8771e9442c21cf51fc1a140c3216">00093</a>         std::vector&lt;Residue&gt; <a class="code" href="classmoltk_1_1PDBStructure_1_1Chain.html#a759a8771e9442c21cf51fc1a140c3216">residues</a>;
<a name="l00094"></a>00094     };
<a name="l00095"></a>00095 
<a name="l00096"></a>00096 <span class="keyword">public</span>:
<a name="l00097"></a><a class="code" href="classmoltk_1_1PDBStructure.html#a855b6bcd33c82b21ebdc4c0f2c0cea6a">00097</a>     <a class="code" href="classmoltk_1_1PDBStructure.html#a855b6bcd33c82b21ebdc4c0f2c0cea6a">PDBStructure</a>() {}
<a name="l00098"></a>00098     <span class="keyword">explicit</span> <a class="code" href="classmoltk_1_1PDBStructure.html#a855b6bcd33c82b21ebdc4c0f2c0cea6a">PDBStructure</a>(std::istream&amp;);
<a name="l00099"></a>00099     <span class="keyword">explicit</span> <a class="code" href="classmoltk_1_1PDBStructure.html#a855b6bcd33c82b21ebdc4c0f2c0cea6a">PDBStructure</a>(<span class="keyword">const</span> std::string&amp; file_name);
<a name="l00100"></a><a class="code" href="classmoltk_1_1PDBStructure.html#adcf055acb239adf14d980333c89d8da0">00100</a>     <a class="code" href="classmoltk_1_1PDBStructure.html#a855b6bcd33c82b21ebdc4c0f2c0cea6a">PDBStructure</a>(<span class="keyword">const</span> <a class="code" href="classmoltk_1_1PDBStructure.html" title="PDBStructure represents a macromolecule structure as found in a Protein Data Bank file...">PDBStructure</a>&amp; rhs)
<a name="l00101"></a>00101         : <a class="code" href="classmoltk_1_1PDBStructure.html#aa339055bdae2959af8baa08363630be5">atoms</a>(rhs.<a class="code" href="classmoltk_1_1PDBStructure.html#aa339055bdae2959af8baa08363630be5">atoms</a>)
<a name="l00102"></a>00102         , <a class="code" href="classmoltk_1_1PDBStructure.html#a1bcb7d83816e73d4bc21fbb46ce27220">chains</a>(rhs.<a class="code" href="classmoltk_1_1PDBStructure.html#a1bcb7d83816e73d4bc21fbb46ce27220">chains</a>)
<a name="l00103"></a>00103     {}
<a name="l00104"></a>00104     <span class="keywordtype">bool</span> <a class="code" href="classmoltk_1_1PDBStructure.html#a216700e937feb8857f30d1626d5ab9cf">load_stream</a>(std::istream&amp;);
<a name="l00105"></a>00105     <span class="keywordtype">bool</span> <a class="code" href="classmoltk_1_1PDBStructure.html#a4891c9ebd0345e15da4e30086628967d">load_file</a>(<span class="keyword">const</span> std::string&amp; file_name);
<a name="l00106"></a>00106 
<a name="l00107"></a>00107 <span class="keyword">protected</span>:
<a name="l00108"></a><a class="code" href="classmoltk_1_1PDBStructure.html#aa339055bdae2959af8baa08363630be5">00108</a>     <a class="code" href="classmoltk_1_1PDBStructure.html#ad5de261e14b5095d93a495e27351777b">AtomList</a> <a class="code" href="classmoltk_1_1PDBStructure.html#aa339055bdae2959af8baa08363630be5">atoms</a>;
<a name="l00109"></a><a class="code" href="classmoltk_1_1PDBStructure.html#a1bcb7d83816e73d4bc21fbb46ce27220">00109</a>     std::vector&lt;Chain&gt; <a class="code" href="classmoltk_1_1PDBStructure.html#a1bcb7d83816e73d4bc21fbb46ce27220">chains</a>;
<a name="l00110"></a>00110 };
<a name="l00111"></a>00111 
<a name="l00112"></a>00112 } <span class="comment">// namespace moltk</span>
<a name="l00113"></a>00113 
<a name="l00114"></a><a class="code" href="PDBStructure_8hpp.html#abe93e26fbc8e6454356093d9be9b9355">00114</a> <span class="keyword">inline</span> std::istream&amp; <a class="code" href="PDBStructure_8hpp.html#abe93e26fbc8e6454356093d9be9b9355">operator&gt;&gt;</a>(std::istream&amp; is, <a class="code" href="classmoltk_1_1PDBStructure.html" title="PDBStructure represents a macromolecule structure as found in a Protein Data Bank file...">moltk::PDBStructure</a>&amp; structure)
<a name="l00115"></a>00115 {
<a name="l00116"></a>00116     structure.<a class="code" href="classmoltk_1_1PDBStructure.html#a216700e937feb8857f30d1626d5ab9cf">load_stream</a>(is);
<a name="l00117"></a>00117     <span class="keywordflow">return</span> is;
<a name="l00118"></a>00118 }
<a name="l00119"></a>00119 
<a name="l00120"></a>00120 
<a name="l00121"></a>00121 <span class="preprocessor">#endif // MOLTK_PDB_STRUCTURE_H</span>
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